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Sample GSM4618802 Query DataSets for GSM4618802
Status Public on Nov 29, 2022
Title C21_spleen_isotype [scRNA-seq]
Sample type SRA
Source name P14 CD8+ T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: P14 CD8+ T cells
treatment: Isotype
disease state: Chronic viral infection
Extracted molecule total RNA
Extraction protocol By using fluorescence-activated cell sorting, CD8+ T cells were obtained from the spleens or lungs of chronic virus-infected mice and from the subcutaneous tumor tissues or metastatic lungs of tumor-engrafted mice. Then, the CD8+ T cells were performed with single-cell RNA-seq library construction.
For single-cell RNA-seq library construction, the libraries were prepared using Chromium Next GEM Single Cell 3’ reagent Kits (10x Genomics) according to the manufacturer’s instructions. Briefly, sorted CD8 T cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, followed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description scRNA Sample 4
Single-cell RNA-seq
Data processing scRNA-seq: The scRNA-seq reads were aligned to the mm10 reference genome and quantified using the cellranger count (10X Genomics, version 3.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: For both scATAC and scRNA-seq, the filtered matrix output folder from the 10X pipeline of each sample is provided as a tar archive.
Submission date Jun 16, 2020
Last update date May 24, 2023
Contact name Jun Huang
Phone 7737023218
Organization name University of Chicago
Department Institute for Molecular Engineering
Lab Huang Lab
Street address Eckhardt, 5640 S Ellis Ave
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platform ID GPL24247
Series (2)
GSE152618 Disease-specific exhaustion features and PD-1 immunotherapy responsiveness of antigen-specific CD8+ T cells at single-cell resolution [scRNA-seq]
GSE152628 Disease-specific exhaustion features and PD-1 immunotherapy responsiveness of antigen-specific CD8+ T cells at single-cell resolution
BioSample SAMN15253665
SRA SRX8557771

Supplementary file Size Download File type/resource
GSM4618802_scRNA_C21_spleen_isotype.tar.gz 69.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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